I think the main problem is that most people don't like stuff on their back, and normal bottles do the trick for them. In another thread I saw the idea of putting a water bag in the bar bag.
Hygiene is certainly an issue, if you want to put anything else than water in it.
As a recumbent rider, I have used a water bag(not from CamelBak, but from MSR) *and* bottles(from CamelBak). The water bag is for water, the bottles are for sugary stuff.
Even with just the use of water, my drinking hose will often get all kinds of interesting colors that I can't get out(ok, I shouldn't leave it around in my kitchen for a week). Buying another new one is on my list.